[Bioc-devel] daily package check - namespace or shadowing problems

[Wolfgang Huber]

Hi all,

I am broadcasting this to bioc-devel because I suspect that several
package maintainers currently are puzzled by similar problems, and as
the saying goes, "shared pain is half the pain" :)

1.) The bioc daily check results for 'vsn' say sth like:

* creating vignettes ... ERROR
Error:  chunk 16 (label=affy1)
Error in update.default(pbt) : need an object with call component
Error in buildVignettes(dir = ".") : Error:  chunk 16 (label=affy1)
Error in update.default(pbt) : need an object with call component
Execution halted

I suspect that the "update.default" which is complaining here is from
namespace:stats, while the intention of the line
   update(pbt)
in affy::AffyBatch.R is apparently to call an "update" method for the
ProgressBarText method defined in that package.

2.) When I am doing "R CMD check vsn" on my local machine, the
compilation of the vignette fails apparently because the function "vsn"
is called on non-sensical data in the chunk "affy1" (the intention there
is to use the Dilution data from "affydata").

3.) When I run "Sweave" on the package vignette in an interactive
session, everything is fine.

So I suspect that some weird problems are going on R with functions e.g.
from the affy package (or others) due to recent changes with namespaces
and S4 methods, which I still am struggling to learn to understand.

 Cheers
  Wolfgang



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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber